BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 029083
(199 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2BHW|A Chain A, Pea Light-Harvesting Complex Ii At 2.5 Angstrom Resolution
pdb|2BHW|B Chain B, Pea Light-Harvesting Complex Ii At 2.5 Angstrom Resolution
pdb|2BHW|C Chain C, Pea Light-Harvesting Complex Ii At 2.5 Angstrom Resolution
Length = 232
Score = 92.0 bits (227), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 48/88 (54%), Positives = 57/88 (64%), Gaps = 4/88 (4%)
Query: 75 WYGPDRRIFLPEGLLDRSEIPEYLTGEVPGDYGYDPFGLSKKPDDFSKYQAYELIHARWA 134
WYGPDR +L E P YLTGE PGDYG+D GLS P+ FSK + E+IH+RWA
Sbjct: 16 WYGPDRVKYLGP---FSGESPSYLTGEFPGDYGWDTAGLSADPETFSKNRELEVIHSRWA 72
Query: 135 MLGAAGFIIPEAFNKFGANCGPEAVWFK 162
MLGA G + PE ++ G G EAVWFK
Sbjct: 73 MLGALGSVFPELLSRNGVKFG-EAVWFK 99
Score = 31.2 bits (69), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 21/36 (58%)
Query: 108 YDPFGLSKKPDDFSKYQAYELIHARWAMLGAAGFII 143
+DP GL+ P+ F++ + EL + R AM GF +
Sbjct: 161 FDPLGLADDPEAFAELKVKELKNGRLAMFSMFGFFV 196
>pdb|1VCR|A Chain A, An Icosahedral Assembly Of Light-Harvesting Chlorophyll AB
Protein Complex From Pea Thylakoid Membranes
Length = 232
Score = 91.7 bits (226), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 48/88 (54%), Positives = 57/88 (64%), Gaps = 4/88 (4%)
Query: 75 WYGPDRRIFLPEGLLDRSEIPEYLTGEVPGDYGYDPFGLSKKPDDFSKYQAYELIHARWA 134
WYGPDR +L E P YLTGE PGDYG+D GLS P+ FSK + E+IH+RWA
Sbjct: 16 WYGPDRVKYLGP---FSGESPSYLTGEFPGDYGWDTAGLSADPETFSKNRELEVIHSRWA 72
Query: 135 MLGAAGFIIPEAFNKFGANCGPEAVWFK 162
MLGA G + PE ++ G G EAVWFK
Sbjct: 73 MLGALGCVFPELLSRNGVKFG-EAVWFK 99
Score = 31.6 bits (70), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 21/36 (58%)
Query: 108 YDPFGLSKKPDDFSKYQAYELIHARWAMLGAAGFII 143
+DP GL+ P+ F++ + EL + R AM GF +
Sbjct: 161 FDPLGLADDPEAFAELKVKELKNGRLAMFSMFGFFV 196
>pdb|1RWT|A Chain A, Crystal Structure Of Spinach Major Light-harvesting
Complex At 2.72 Angstrom Resolution
pdb|1RWT|B Chain B, Crystal Structure Of Spinach Major Light-harvesting
Complex At 2.72 Angstrom Resolution
pdb|1RWT|C Chain C, Crystal Structure Of Spinach Major Light-harvesting
Complex At 2.72 Angstrom Resolution
pdb|1RWT|D Chain D, Crystal Structure Of Spinach Major Light-harvesting
Complex At 2.72 Angstrom Resolution
pdb|1RWT|E Chain E, Crystal Structure Of Spinach Major Light-harvesting
Complex At 2.72 Angstrom Resolution
pdb|1RWT|F Chain F, Crystal Structure Of Spinach Major Light-harvesting
Complex At 2.72 Angstrom Resolution
pdb|1RWT|G Chain G, Crystal Structure Of Spinach Major Light-harvesting
Complex At 2.72 Angstrom Resolution
pdb|1RWT|H Chain H, Crystal Structure Of Spinach Major Light-harvesting
Complex At 2.72 Angstrom Resolution
pdb|1RWT|I Chain I, Crystal Structure Of Spinach Major Light-harvesting
Complex At 2.72 Angstrom Resolution
pdb|1RWT|J Chain J, Crystal Structure Of Spinach Major Light-harvesting
Complex At 2.72 Angstrom Resolution
Length = 232
Score = 89.0 bits (219), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 47/88 (53%), Positives = 55/88 (62%), Gaps = 4/88 (4%)
Query: 75 WYGPDRRIFLPEGLLDRSEIPEYLTGEVPGDYGYDPFGLSKKPDDFSKYQAYELIHARWA 134
WYGPDR +L E P YLTGE PGDYG+D GLS P+ F+K + E+IH RWA
Sbjct: 16 WYGPDRVKYLGP---FSGESPSYLTGEFPGDYGWDTAGLSADPETFAKNRELEVIHCRWA 72
Query: 135 MLGAAGFIIPEAFNKFGANCGPEAVWFK 162
MLGA G + PE + G G EAVWFK
Sbjct: 73 MLGALGCVFPELLARNGVKFG-EAVWFK 99
Score = 30.8 bits (68), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 21/36 (58%)
Query: 108 YDPFGLSKKPDDFSKYQAYELIHARWAMLGAAGFII 143
+DP GL+ P+ F++ + E+ + R AM GF +
Sbjct: 161 FDPLGLADDPEAFAELKVKEIKNGRLAMFSMFGFFV 196
>pdb|2WSC|2 Chain 2, Improved Model Of Plant Photosystem I
pdb|2WSE|2 Chain 2, Improved Model Of Plant Photosystem I
pdb|2WSF|2 Chain 2, Improved Model Of Plant Photosystem I
Length = 269
Score = 71.2 bits (173), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 34/74 (45%), Positives = 43/74 (58%), Gaps = 5/74 (6%)
Query: 78 PDRRIFLPEGLLDRSEIPEYLTGEVPGDYGYDPFGLSKKPDDFSKYQAYELIHARWAMLG 137
PDR ++ P S P +L G +PGD+G+DP GL P+ EL+H+RWAMLG
Sbjct: 62 PDRPLWFPG-----STPPPWLDGSLPGDFGFDPLGLGSDPESLRWNVQAELVHSRWAMLG 116
Query: 138 AAGFIIPEAFNKFG 151
AAG IPE K G
Sbjct: 117 AAGIFIPEFLTKLG 130
>pdb|2O01|2 Chain 2, The Structure Of A Plant Photosystem I Supercomplex At 3.4
Angstrom Resolution
Length = 186
Score = 70.9 bits (172), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 31/57 (54%), Positives = 38/57 (66%)
Query: 95 PEYLTGEVPGDYGYDPFGLSKKPDDFSKYQAYELIHARWAMLGAAGFIIPEAFNKFG 151
PE+L G +PGD+G+DP GLS P+ EL+H+RWAMLGAAG IPE K G
Sbjct: 1 PEWLDGSLPGDFGFDPLGLSSDPESLRWNVQAELVHSRWAMLGAAGIFIPEFLTKLG 57
>pdb|2WSC|4 Chain 4, Improved Model Of Plant Photosystem I
pdb|2WSE|4 Chain 4, Improved Model Of Plant Photosystem I
pdb|2WSF|4 Chain 4, Improved Model Of Plant Photosystem I
Length = 251
Score = 68.9 bits (167), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 28/57 (49%), Positives = 39/57 (68%)
Query: 95 PEYLTGEVPGDYGYDPFGLSKKPDDFSKYQAYELIHARWAMLGAAGFIIPEAFNKFG 151
P YLTG +PGD G+DP GL++ P++ + EL++ RWAMLG AG ++PE F G
Sbjct: 63 PGYLTGSLPGDNGFDPLGLAEDPENLRWFVQAELVNGRWAMLGVAGMLLPEVFTSIG 119
>pdb|2WSC|1 Chain 1, Improved Model Of Plant Photosystem I
pdb|2WSE|1 Chain 1, Improved Model Of Plant Photosystem I
pdb|2WSF|1 Chain 1, Improved Model Of Plant Photosystem I
Length = 241
Score = 67.0 bits (162), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 27/53 (50%), Positives = 35/53 (66%)
Query: 95 PEYLTGEVPGDYGYDPFGLSKKPDDFSKYQAYELIHARWAMLGAAGFIIPEAF 147
P YL G PGD+G+DP GL + P + +Y+ ELIH RWAML G ++PEA
Sbjct: 55 PAYLDGSAPGDFGFDPLGLGEVPANLERYKESELIHCRWAMLAVPGILVPEAL 107
Score = 30.0 bits (66), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 21/39 (53%)
Query: 108 YDPFGLSKKPDDFSKYQAYELIHARWAMLGAAGFIIPEA 146
+DP G SK P + + E+ + R A+L GF + ++
Sbjct: 172 FDPLGYSKDPKKLEELKVKEIKNGRLALLAFVGFCVQQS 210
>pdb|2O01|1 Chain 1, The Structure Of A Plant Photosystem I Supercomplex At 3.4
Angstrom Resolution
Length = 187
Score = 66.2 bits (160), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 27/53 (50%), Positives = 35/53 (66%)
Query: 95 PEYLTGEVPGDYGYDPFGLSKKPDDFSKYQAYELIHARWAMLGAAGFIIPEAF 147
P YL G PGD+G+DP GL + P + +Y+ ELIH RWAML G ++PEA
Sbjct: 7 PAYLDGSAPGDFGFDPLGLGEVPANLERYKESELIHCRWAMLAVPGILVPEAL 59
Score = 29.6 bits (65), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 21/39 (53%)
Query: 108 YDPFGLSKKPDDFSKYQAYELIHARWAMLGAAGFIIPEA 146
+DP G SK P + + E+ + R A+L GF + ++
Sbjct: 124 FDPLGYSKDPKKLEELKVKEIKNGRLALLAFVGFCVQQS 162
>pdb|3LW5|1 Chain 1, Improved Model Of Plant Photosystem I
Length = 170
Score = 58.9 bits (141), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 23/47 (48%), Positives = 31/47 (65%)
Query: 102 VPGDYGYDPFGLSKKPDDFSKYQAYELIHARWAMLGAAGFIIPEAFN 148
PGD+G+DP GL + P + +Y+ ELIH RWAML G ++PEA
Sbjct: 2 APGDFGFDPLGLGEVPANLERYKESELIHCRWAMLAVPGILVPEALG 48
Score = 30.0 bits (66), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 21/39 (53%)
Query: 108 YDPFGLSKKPDDFSKYQAYELIHARWAMLGAAGFIIPEA 146
+DP G SK P + + E+ + R A+L GF + ++
Sbjct: 112 FDPLGYSKDPKKLEELKVKEIKNGRLALLAFVGFCVQQS 150
>pdb|2WSC|3 Chain 3, Improved Model Of Plant Photosystem I
pdb|2WSE|3 Chain 3, Improved Model Of Plant Photosystem I
pdb|2WSF|3 Chain 3, Improved Model Of Plant Photosystem I
Length = 276
Score = 53.1 bits (126), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 34/76 (44%), Positives = 43/76 (56%), Gaps = 8/76 (10%)
Query: 96 EYLTGEVPGDYGYDPFGLSKKPDDFS-----KYQAY-ELIHARWAMLGAAGFIIPEAFNK 149
YL G +PGDYG+DP GLS P+ K+ AY E+I+ R+AMLGA G I PE K
Sbjct: 67 SYLDGSLPGDYGFDPLGLS-DPEGTGGFIEPKWLAYGEIINGRYAMLGAVGAIAPEILGK 125
Query: 150 FGANCGPEAV-WFKVN 164
G A+ WF+
Sbjct: 126 AGLIPQETALPWFRTG 141
>pdb|3LW5|4 Chain 4, Improved Model Of Plant Photosystem I
Length = 166
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 27/45 (60%)
Query: 113 LSKKPDDFSKYQAYELIHARWAMLGAAGFIIPEAFNKFGANCGPE 157
L++ P++ + EL++ RWAMLG AG ++PE F G P+
Sbjct: 1 LAEDPENLRWFVQAELVNGRWAMLGVAGMLLPEVFTSIGIINVPK 45
>pdb|3LW5|2 Chain 2, Improved Model Of Plant Photosystem I
Length = 176
Score = 40.8 bits (94), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 17/25 (68%), Positives = 19/25 (76%)
Query: 127 ELIHARWAMLGAAGFIIPEAFNKFG 151
EL+H+RWAMLGAAG IPE K G
Sbjct: 13 ELVHSRWAMLGAAGIFIPEFLTKLG 37
>pdb|3PL9|A Chain A, Crystal Structure Of Spinach Minor Light-Harvesting
Complex Cp29 At 2.80 Angstrom Resolution
Length = 243
Score = 40.0 bits (92), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 30/101 (29%), Positives = 38/101 (37%), Gaps = 45/101 (44%)
Query: 92 SEIPEYLTGEVPGDYGYDPFGLSKKPDDFSKY---------------------------- 123
++ PEYL G + GDYG+DPFGL KP ++ +Y
Sbjct: 18 AKAPEYLDGSLVGDYGFDPFGLG-KPAEYLQYDYDGLDQNLAKNLAGDIIGTRTESADVK 76
Query: 124 ----QAY------------ELIHARWAMLGAAGFIIPEAFN 148
Q Y ELIH RWAML G + E
Sbjct: 77 STSLQPYSEVFGLQRFRECELIHGRWAMLATLGALTVEGLT 117
Score = 34.7 bits (78), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 23/44 (52%)
Query: 108 YDPFGLSKKPDDFSKYQAYELIHARWAMLGAAGFIIPEAFNKFG 151
+DP GL+ P+ Q E+ HAR AM+G GF + A G
Sbjct: 178 FDPLGLASDPEKKPILQLAEIKHARLAMVGFLGFAVQAAVTGKG 221
>pdb|2O01|4 Chain 4, The Structure Of A Plant Photosystem I Supercomplex At 3.4
Angstrom Resolution
Length = 165
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 24/41 (58%)
Query: 117 PDDFSKYQAYELIHARWAMLGAAGFIIPEAFNKFGANCGPE 157
P++ + EL++ RWAMLG AG ++PE F G P+
Sbjct: 1 PENLRWFVQAELVNGRWAMLGVAGMLLPEVFTSIGIINVPK 41
>pdb|2O01|3 Chain 3, The Structure Of A Plant Photosystem I Supercomplex At 3.4
Angstrom Resolution
Length = 165
Score = 32.7 bits (73), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 127 ELIHARWAMLGAAGFIIPEAFNKFGANCGPEAV-WFKVNL 165
E+I+ R+AMLGAAG I PE K G A+ WF+ +
Sbjct: 6 EIINGRFAMLGAAGAIAPEILGKAGLIPAETALPWFQTGV 45
>pdb|3LW5|3 Chain 3, Improved Model Of Plant Photosystem I
Length = 172
Score = 30.8 bits (68), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 19/46 (41%), Positives = 27/46 (58%), Gaps = 2/46 (4%)
Query: 122 KYQAY-ELIHARWAMLGAAGFIIPEAFNKFGANCGPEAV-WFKVNL 165
++ AY E+I+ R+AMLGA G I PE K G A+ WF+ +
Sbjct: 13 RWLAYGEVINGRFAMLGAVGAIAPEYLGKVGLIPQETALAWFQTGV 58
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.321 0.139 0.445
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,408,335
Number of Sequences: 62578
Number of extensions: 211430
Number of successful extensions: 373
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 342
Number of HSP's gapped (non-prelim): 28
length of query: 199
length of database: 14,973,337
effective HSP length: 94
effective length of query: 105
effective length of database: 9,091,005
effective search space: 954555525
effective search space used: 954555525
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)